0
the knowledge web




       13 november 2008

     ucla graduate school of
education and information sciences
knowledge gaps
  process failures
 transaction costs
lost opportunities
knowledge gaps
                  process failures
                 transaction costs
                lost opportunities


...
many information
products advance
  incrementally
the discovery process:
the discovery process:
thanks to the products,
we already know a lot...
we need information innovations
    and process innovations
 to match product innovations.
1.
  the “digital commons” represents a
 methodology that lowers the cost and
increases the volume of transactions
at the ...
does the ability to ask more
questions, faster, lead us to more
 knowledge or just more data?
what’s different about
communications and computers?
1. we know stuff.
1. we know stuff.
2. open networks.
content

 code

physical
content

 code

physical
knowledge

 content

  code

 physical
knowledge rights
knowledge rights
“the commons”
“digital commons”

   interoperability
low transaction costs
 law and technology
user interface to copyright
140,000,000+ digital objects online
       under our licenses

licenses “ported” to 50+ countries

  integrated with Googl...
2.
  the digital commons is a stable
 methodology to manage data,
materials, and content for science.
project development   “do no harm”


 funding
pro bono                                           “running code”
community
...
what would move via the science network?
Open Access Content
making knowledge legally and
technically available for re-use and
composition into new knowledge.
we use digital
tools to replicate
paper technology
©
creative expression
©
ideas or facts
e=mc2
the container, not the facts.
the container, not the facts.

but   © locks the container.
IGFBP-5 plays a role in the
regulation of cellular senescence
via a p53-dependent pathway
and in aging-associated vascular...
IGFBP-5 plays a role in the
regulation of cellular senescence
via a p53-dependent pathway
and in aging-associated vascular...
indexing: disallowed.




  http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
c
>1000 journals under CC

  image from the public library of science
  licensed to the public under CC-BY 3.0
PubMedCentral ~ 1,000,000 articles
      permissions granted: 50,000
(6% of PMC legal for transformative use)
      (.003 ...
what do these
      ideas mean in
a world of integrated data?
creative
 work?
“So, out of all of this
   discussion my
question is whether
   ChemSpider is
Content or Data.” -
  Antony Williams
“The motivation behind this memorandum is
     interoperability of scientific data.”
+

is it legal?
+        +         +




+   is it legal?   +




+         +        +
1 Converge on the public domain by waiving all rights
based on intellectual property


2 Converge on the public domain by ...
a protocol, not a license.
conflicts with the protection instinct
conflicts with the protection instinct
the protection instinct is frequently an instinct to protect “freedom”
3.
we have to build infrastructure for data
into the web of documents that we have.
solves the legal problem
but not the
container problem.
web 2.0, science 3.0, what about
 making Google work better?
over 200
   years at
one paper/day
what you want is
   a list of genes.

not a list of documents.
building a web for data:
  the “semantic web”
making computers understand links between documents




                     links to
    Web page                        ...
making computers understand relationships between concepts




                        causes
     drinking coffee        ...
causes
drink coffee            feel awake
http://ontology.foo.org/causes



                                          causes
          drinking coffee              ...
we need a Domain Name System for concepts:

192.168.1.1             http://sciencecommons.org

  coffee                htt...
use the web to
           integrate information
            from different places
             and different names
“coffee...
bed
                                                                                    person

 located at               ...
(too much work for
      coffee)
(distributed, networked
  approaches start to
   look pretty good)
Open Source
Data Integration
formatting digital knowledge into
   modular building blocks for
composition into new knowledge.
e pluribus unum.
we can transform complex queries into links


            prefix go: <http://purl.org/obo/owl/GO#>
    prefix rdfs: <http:...
we can transform complex queries into links
http://hcls1.csail.mit.edu:8890/sparql/?query=prefix%20go%3A%20%3Chttp%3A%2F%2F...
we can transform complex queries into links
we can help scholars “remix” queries
   prefix go: <http://purl.org/obo/owl/GO#>
   prefix rdfs: <http://www.w3.org/2000/01/...
we can build a corpus of queries as links
we can re-use cultural tools for scholarship
we can make science user-driven.
4.
institutions have to provide a stable
  foundation for the knowledge web.
process revolutions: the network
                         Huntington’s


Parkinson’s




                                 ...
institutional revolutions: the network
                      Huntington’s


 Parkinson’s




                             ...
the library to me:
location, structure, discovery, preservation
the infrastructure for this is very, very shaky.
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix skos: <http://www.w3.org/2004/02/skos/core#>
prefix rdfs: <http://www.w3...
what are the odds that the organizations making the
 namespaces will be here in 50 years? 100 years?
Huntington’s
Huntington’s


Parkinson’s




                                ALS




     Multiple
     Sclerosis


                 Aut...
Huntington’s


Parkinson’s




                 library
                                          ALS




     Multiple
  ...
“In any case, it is clear that a library containing all possible
 books, arranged at random, is equivalent (as a source of...
exponential content growth
our brain capacity


5.00



3.75



2.50



1.25



  0
   1990   1994                    1998   2002
1.	Books are for use.
	   2. Every reader his [or her] book.
	   3. Every book its reader.
	   4. Save the time of the Use...
1.	Books are for use.
	   2. Every reader his [or her] book.
	   3. Every book its reader.
	   4. Save the time of the Use...
call to action:

1. join up with the semantic people - support discipline-driven
                  namespaces and ontologi...
thank you

wilbanks@creativecommons.org

  http://sciencecommons.org
Ucla GSEIS
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  1. 1. the knowledge web 13 november 2008 ucla graduate school of education and information sciences
  2. 2. knowledge gaps process failures transaction costs lost opportunities
  3. 3. knowledge gaps process failures transaction costs lost opportunities is the answer more information?
  4. 4. many information products advance incrementally
  5. 5. the discovery process:
  6. 6. the discovery process:
  7. 7. thanks to the products, we already know a lot...
  8. 8. we need information innovations and process innovations to match product innovations.
  9. 9. 1. the “digital commons” represents a methodology that lowers the cost and increases the volume of transactions at the “knowledge layer” of the net
  10. 10. does the ability to ask more questions, faster, lead us to more knowledge or just more data?
  11. 11. what’s different about communications and computers?
  12. 12. 1. we know stuff.
  13. 13. 1. we know stuff. 2. open networks.
  14. 14. content code physical
  15. 15. content code physical
  16. 16. knowledge content code physical
  17. 17. knowledge rights
  18. 18. knowledge rights
  19. 19. “the commons”
  20. 20. “digital commons” interoperability low transaction costs law and technology
  21. 21. user interface to copyright
  22. 22. 140,000,000+ digital objects online under our licenses licenses “ported” to 50+ countries integrated with Google,Yahoo, Firefox, Microsoft Office...
  23. 23. 2. the digital commons is a stable methodology to manage data, materials, and content for science.
  24. 24. project development “do no harm” funding pro bono “running code” community “think market” early focus on life sciences exploring climate change, geospatial, elsewhere
  25. 25. what would move via the science network?
  26. 26. Open Access Content
  27. 27. making knowledge legally and technically available for re-use and composition into new knowledge.
  28. 28. we use digital tools to replicate paper technology
  29. 29. © creative expression
  30. 30. © ideas or facts
  31. 31. e=mc2
  32. 32. the container, not the facts.
  33. 33. the container, not the facts. but © locks the container.
  34. 34. IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
  35. 35. IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
  36. 36. indexing: disallowed. http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
  37. 37. c >1000 journals under CC image from the public library of science licensed to the public under CC-BY 3.0
  38. 38. PubMedCentral ~ 1,000,000 articles permissions granted: 50,000 (6% of PMC legal for transformative use) (.003 of all PubMed records)
  39. 39. what do these ideas mean in a world of integrated data?
  40. 40. creative work?
  41. 41. “So, out of all of this discussion my question is whether ChemSpider is Content or Data.” - Antony Williams
  42. 42. “The motivation behind this memorandum is interoperability of scientific data.”
  43. 43. + is it legal?
  44. 44. + + + + is it legal? + + + +
  45. 45. 1 Converge on the public domain by waiving all rights based on intellectual property 2 Converge on the public domain by waiving other statutory or intellectual property rights. 3 Converge on the public domain by imposing no contractual controls. 4 Provide for interoperation with databases not available under the Protocol through open metadata
  46. 46. a protocol, not a license.
  47. 47. conflicts with the protection instinct
  48. 48. conflicts with the protection instinct the protection instinct is frequently an instinct to protect “freedom”
  49. 49. 3. we have to build infrastructure for data into the web of documents that we have.
  50. 50. solves the legal problem
  51. 51. but not the container problem.
  52. 52. web 2.0, science 3.0, what about making Google work better?
  53. 53. over 200 years at one paper/day
  54. 54. what you want is a list of genes. not a list of documents.
  55. 55. building a web for data: the “semantic web”
  56. 56. making computers understand links between documents links to Web page Web page
  57. 57. making computers understand relationships between concepts causes drinking coffee feel awake
  58. 58. causes drink coffee feel awake
  59. 59. http://ontology.foo.org/causes causes drinking coffee feel awake http://ontology.foo.org/drinking coffee http://ontology.foo.org/feel awake h
  60. 60. we need a Domain Name System for concepts: 192.168.1.1 http://sciencecommons.org coffee http://ontology.foo.org/coffee
  61. 61. use the web to integrate information from different places and different names “coffee” “cafe” coffee http://ontology.foo.org/coffee “kopi”
  62. 62. bed person located at get out of bed last subevent does not want wants get out of bed after causes drink coffee feel awake first subevent subevent causes feel jittery open eyes after after make coffee pour coffee pick up cup drink is a is for located in coffee cafe property of often near often near wet cup sugar
  63. 63. (too much work for coffee)
  64. 64. (distributed, networked approaches start to look pretty good)
  65. 65. Open Source Data Integration
  66. 66. formatting digital knowledge into modular building blocks for composition into new knowledge.
  67. 67. e pluribus unum.
  68. 68. we can transform complex queries into links prefix go: <http://purl.org/obo/owl/GO#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> Mesh: Pyramidal Neurons prefix owl: <http://www.w3.org/2002/07/owl#> prefix mesh: <http://purl.org/commons/record/mesh/> prefix sc: <http://purl.org/science/owl/sciencecommons/> prefix ro: <http://www.obofoundry.org/ro/ro.owl#> select ?genename ?processname where { graph <http://purl.org/commons/hcls/pubmesh> Pubmed: Journal Articles { ?paper ?p mesh:D017966 . ?article sc:identified_by_pmid ?paper. ?gene sc:describes_gene_or_gene_product_mentioned_by ?article. } graph <http://purl.org/commons/hcls/goa> Entrez Gene: Genes { ?protein rdfs:subClassOf ?res. ?res owl:onProperty ro:has_function. ?res owl:someValuesFrom ?res2. ?res2 owl:onProperty ro:realized_as. ?res2 owl:someValuesFrom ?process. graph <http://purl.org/commons/hcls/20070416/classrelations> {{?process <http://purl.org/obo/owl/obo#part_of> go:GO_0007166} union {?process rdfs:subClassOf go:GO_0007166 }} ?protein rdfs:subClassOf ?parent. ?parent owl:equivalentClass ?res3. GO: Signal Transduction ?res3 owl:hasValue ?gene. } graph <http://purl.org/commons/hcls/gene> { ?gene rdfs:label ?genename } graph <http://purl.org/commons/hcls/20070416> { ?process rdfs:label ?processname} }
  69. 69. we can transform complex queries into links http://hcls1.csail.mit.edu:8890/sparql/?query=prefix%20go%3A%20%3Chttp%3A%2F%2Fpurl.org%2Fobo%2Fowl%2FGO%23%3E%0Aprefix%20rdfs%3A %20%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0Aprefix%20owl%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F2002% 2F07%2Fowl%23%3E%0Aprefix%20mesh%3A%20%3Chttp%3A%2F%2Fpurl.org%2Fcommons%2Frecord%2Fmesh%2F%3E%0Aprefix%20sc%3A%20% 3Chttp%3A%2F%2Fpurl.org%2Fscience%2Fowl%2Fsciencecommons%2F%3E%0Aprefix%20ro%3A%20%3Chttp%3A%2F%2Fwww.obofoundry.org%2Fro %2Fro.owl%23%3E%0A%0Aselect%20%3Fgenename%20%3Fprocessname%0Awhere%0A%7B%20%20graph%20%3Chttp%3A%2F%2Fpurl.org% 2Fcommons%2Fhcls%2Fpubmesh%3E%0A%20%20%20%20%20%7B%20%3Fpaper%20%3Fp%20mesh%3AD017966%20.%0A%20%20%20%20%20%20% 20%3Farticle%20sc%3Aidentified_by_pmid%20%3Fpaper.%0A%20%20%20%20%20%20%20%3Fgene%20sc% 3Adescribes_gene_or_gene_product_mentioned_by%20%3Farticle.%0A%20%20%20%20%20%7D%0A%20%20%20graph%20%3Chttp%3A%2F% 2Fpurl.org%2Fcommons%2Fhcls%2Fgoa%3E%0A%20%20%20%20%20%7B%20%3Fprotein%20rdfs%3AsubClassOf%20%3Fres.%0A%20%20%20%20% 20%20%20%3Fres%20owl%3AonProperty%20ro%3Ahas_function.%0A%20%20%20%20%20%20%20%3Fres%20owl%3AsomeValuesFrom%20%3Fres2.% 0A%20%20%20%20%20%20%20%3Fres2%20owl%3AonProperty%20ro%3Arealized_as.%0A%20%20%20%20%20%20%20%3Fres2%20owl% 3AsomeValuesFrom%20%3Fprocess.%0A%20%20%20graph%20%3Chttp%3A%2F%2Fpurl.org%2Fcommons%2Fhcls%2F20070416%2Fclassrelations%3E %0A%20%20%20%20%20%7B%7B%3Fprocess%20%3Chttp%3A%2F%2Fpurl.org%2Fobo%2Fowl%2Fobo%23part_of%3E%20go%3AGO_0007166%7D% 0A%20%20%20%20%20%20%20union%0A%20%20%20%20%20%20%7B%3Fprocess%20rdfs%3AsubClassOf%20go%3AGO_0007166%20%7D%7D%0A %20%20%20%20%20%20%20%3Fprotein%20rdfs%3AsubClassOf%20%3Fparent.%0A%20%20%20%20%20%20%20%3Fparent%20owl% 3AequivalentClass%20%3Fres3.%0A%20%20%20%20%20%20%20%3Fres3%20owl%3AhasValue%20%3Fgene.%0A%20%20%20%20%20%20%7D%0A% 20%20%20graph%20%3Chttp%3A%2F%2Fpurl.org%2Fcommons%2Fhcls%2Fgene%3E%0A%20%20%20%20%20%7B%20%3Fgene%20rdfs%3Alabel%20% 3Fgenename%20%7D%0A%20%20%20graph%20%3Chttp%3A%2F%2Fpurl.org%2Fcommons%2Fhcls%2F20070416%3E%0A%20%20%20%20%20%7B% 20%3Fprocess%20rdfs%3Alabel%20%3Fprocessname%7D%0A%7D&format=&maxrows=50
  70. 70. we can transform complex queries into links
  71. 71. we can help scholars “remix” queries prefix go: <http://purl.org/obo/owl/GO#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix owl: <http://www.w3.org/2002/07/owl#> prefix mesh: <http://purl.org/commons/record/mesh/> prefix sc: <http://purl.org/science/owl/sciencecommons/> prefix ro: <http://www.obofoundry.org/ro/ro.owl#> select ?genename ?processname where { graph <http://purl.org/commons/hcls/pubmesh> mesh:D009369 { ?paper ?p ?article sc:identified_by_pmid ?paper. . Mesh: Cancer ?gene sc:describes_gene_or_gene_product_mentioned_by ?article. } graph <http://purl.org/commons/hcls/goa> { ?protein rdfs:subClassOf ?res. ?res owl:onProperty ro:has_function. ?res owl:someValuesFrom ?res2. ?res2 owl:onProperty ro:realized_as. ?res2 owl:someValuesFrom ?process. graph <http://purl.org/commons/hcls/20070416/classrelations> {{?process <http://purl.org/obo/owl/obo#part_of> go:GO_0006610} union go:GO_0006610 }} {?process rdfs:subClassOf ?protein rdfs:subClassOf ?parent. GO: Ribosomal Protein ?parent owl:equivalentClass ?res3. ?res3 owl:hasValue ?gene. } graph <http://purl.org/commons/hcls/gene> { ?gene rdfs:label ?genename } graph <http://purl.org/commons/hcls/20070416> { ?process rdfs:label ?processname} }
  72. 72. we can build a corpus of queries as links
  73. 73. we can re-use cultural tools for scholarship
  74. 74. we can make science user-driven.
  75. 75. 4. institutions have to provide a stable foundation for the knowledge web.
  76. 76. process revolutions: the network Huntington’s Parkinson’s ALS Multiple Sclerosis Autism
  77. 77. institutional revolutions: the network Huntington’s Parkinson’s ALS Multiple Sclerosis Autism
  78. 78. the library to me: location, structure, discovery, preservation
  79. 79. the infrastructure for this is very, very shaky.
  80. 80. prefix dc: <http://purl.org/dc/elements/1.1/> prefix skos: <http://www.w3.org/2004/02/skos/core#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix owl: <http://www.w3.org/2002/07/owl#> prefix sc: <http://purl.org/science/owl/sciencecommons/> prefix foaf: <http://xmlns.com/foaf/0.1/>
  81. 81. what are the odds that the organizations making the namespaces will be here in 50 years? 100 years?
  82. 82. Huntington’s
  83. 83. Huntington’s Parkinson’s ALS Multiple Sclerosis Autism
  84. 84. Huntington’s Parkinson’s library ALS Multiple Sclerosis Autism
  85. 85. “In any case, it is clear that a library containing all possible books, arranged at random, is equivalent (as a source of information) to a library containing zero books.” http://en.wikipedia.org/wiki/The_Library_of_Babel
  86. 86. exponential content growth
  87. 87. our brain capacity 5.00 3.75 2.50 1.25 0 1990 1994 1998 2002
  88. 88. 1. Books are for use. 2. Every reader his [or her] book. 3. Every book its reader. 4. Save the time of the User. 5. The library is a growing organism.
  89. 89. 1. Books are for use. 2. Every reader his [or her] book. 3. Every book its reader. 4. Save the time of the User. 5. The library is a growing organism. what’s the digital version of the five laws?
  90. 90. call to action: 1. join up with the semantic people - support discipline-driven namespaces and ontologies 2. queries are the interface - average user doesn’t know how to ask complicated questions on the research web. 3. make the library the hub of the research web.
  91. 91. thank you wilbanks@creativecommons.org http://sciencecommons.org
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